The PCA and LDA analysis on the differential expression of proteins in breast cancer

Disease Markers

Volumn 29, Issue 5, 2010, Pages 231-242

  Liang, Seng ^a   Singh, Manjit ^b   Dharmaraj, Saravanan ^a   Gam, Lay Harn ^a  

^a SCHOOL OF PHARMACEUTICAL SCIENCES   (Malaysia)

^b HOSPITAL PULAU PINANG   (Malaysia)

Author keywords

biomarkers; Breast cancer; LDA; PCA; proteomics

Indexed keywords

APOLIPOPROTEIN A1; BIOLOGICAL MARKER; CALRETICULIN; FIBRINOGEN; ISOPROTEIN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; TUMOR MARKER;

ADULT; AGED; ARTICLE; BETA CHAIN; BETA RHYTHM; BREAST CANCER; CLINICAL ARTICLE; CONTROLLED STUDY; DIFFERENTIAL DISPLAY; FEMALE; HUMAN; HUMAN TISSUE; MALAYSIA; MORTALITY; NUCLEOTIDE SEQUENCE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS;

EID: 79951526112     PISSN: 02780240     EISSN: None     Source Type: Journal    
DOI: 10.3233/DMA-2010-0753     Document Type: Article

References (58)

1. World Health Organization, Cancer: Fact Sheet, [updated February 2009], 2009. Available from: http://www.who.int/entity/mediacentre/factsheets/fs297/en/ index.html.
2. World Health Organization, Breast Cancer Burden, 2010. Available from: http://www.who.int/cancer/detection/breastcancer/en/index1.html.
3. Malaysian Oncological Society and Breast Cancer 2010. Available from: http://www.malaysiaoncology.org/article.php?aid=114
4. R.B. Dickson, R.G. Pestell and M.E. Lippman, Cancer of the breast, in: Cancer - Principals and Practice of Oncology, V.T. Devita and S.A. Rosenberg, eds, Lippincott Williams and Wilkins, Philadelphia, 2005, pp. 1399-1487.
5. M.R. Wilkins, C. Pasquali, R.D. Appel, K. Ou, O. Golaz, J.C. Sanchez, J.X. Yan, A.A. Gooley, G. Hughes, I. Humphrey-Smith, K.L. Williams and D.F. Hochstrasser, From protein to proteomics: large-scale protein identification by two-dimensional electrophoresis and amino acid analysis, Biotechnology 14 (1996), 61-65.
6. C.S. Giometti, S.L. Tollaksen, C. Chubb, C. Williams and E. Huberman, Analysis of proteins from human breast epithelial cells using two-dimensional gel electrophoresis, Elec-trophoresis 16 (1995), 1215-1224.
7. S. Liang, M. Singh and L.H. Gam, The differential expression of aqueous soluble proteins in breast normal and cancerous tissues in relation to ethnicity of the patients; Chinese, Malay and Indian, Disease Markers 28 (2010), 149-165.
8. F. Le Naour, D.E. Misek, M.C. Krause, L. Deneux, T.J. Giordano, S. Scholl and S.M. Hamash, Proteomics-based identification of RS/DJ-1 as a novel circulating tumour antigen in breast cancer, Clin Cancer Res 7 (2001), 3325-3327.
9. D.Q. Li, L. Wang, F. Fei, Y.F. Hou, J.M. Luo, Wei Chen, R. Zeng, J. Wu, J.S. Lu, G.H. Di, Z.L. Ou, Q. Xia, Z.Z. Shen and Z.M. Shao, Identification of breast cancer metastasis-associated proteins in an isogenic tumor metastasis model using two-dimensional gel electrophoresis and liquid chromatography-ion trap-mass spectrometry, Proteomics 6 (2006), 3352-3368. (Pubitemid 43886152)
10. M.J. Page, B. Amess, R.R. Townsend, R. Parekh, A. Herath, L. Brusten, M.J. Zvelebil, R.C. Stein, M.D. Waterfield, S.C. Davies and M.J. O'Hare, Proteomic definition of normal human luminal and myoepithelial breast cells purified from reduction mammoplasties, Proc Natl Acad Sci USA 96 (1999), 12589-12594. (Pubitemid 29513546)
11. K. Williams, C. Chubb, E. Hubermann and C.S. Giometti, Analysis of differential protein expression in normal and neo-plastic human breast epithelial cell lines, Electrophoresis 19 (1998), 333-343. (Pubitemid 28131260)
12. P. Alfonso, A. Nuñez, J. Madoz-Gurpide, L. Lombardia, L. Sanchez and J.I. Casal, Proteomic expression analysis of colorectal cancer by two-dimensional differential gel elec-trophoresis, Proteomics 5 (2005), 2602-2611. (Pubitemid 40966487)
13. R. Chen, S. Pan, T.A. Bretnall and R. Aebersold, Proteomic profiling of pancreatic cancer for biomarker discovery, Mol Cell Proteomics 4 (2005), 523-533. (Pubitemid 40590569)
14. D.B. Friedman, S. Hill, J.W. Keller, N.B. Merchant, S.E. Levy, R.J. Coffey and R.M. Caprioli, Proteome analysis of human colon cancer by two-dimensional difference gel electrophore-sis and mass spectrometry, Proteomics 4 (2004), 793-811. (Pubitemid 38339157)
15. P.R. Jungblut, U. Zimny-Arndt, E. Ziendl-Eberhart, J. Stuĺik, K. Koupilova, K.P. Pleissner, A. Otto, E.C. Müller, W. Sokolowska-Köhler, G. Grabher and G. Stöffler, Proteomics in human disease: cancer, heart and infectious diseases, Elec-trophoresis 20 (1999), 2100-2110. (Pubitemid 29376818)
16. M.R. Emmert-Buck, J.W. Gillespie, C.P. Pawaletz, D.K. Orn-stein, V. Basrur, E. Appella, Q.H. Wang, J. Huang, N. Hu, P. Taylor and E.F. Petricoin, An approach to proteomic analysis of human tumors, Mol Carcinog 27 (2000), 158-165. (Pubitemid 30149311)
17. F.J. Esteva and G.N. Hortobagyi, Prognostic molecular markers in early breast cancer, Breast Cancer Res 6 (2004), 109-118. (Pubitemid 38607664)
18. M.J. Karson, Multivariate statistical methods: An introduction, Iowa State University Press, Iowa, 1982, p. 159, 191.
19. N.C. Giri, Multivariate Statistical Analysis, Marcel Dekker, New York, 1996, p. 293.
20. S.O. Deininger, M.P. Ebert, A. Fütterer, M. Gerhard and C. Röcken, MALDI imaging combined with hierarchical clustering as a new tool for the interpretation of complex human cancers, J Proteome Res 7 (2008), 5230-5236.
21. M.C. Djidja, E.Claude, M. Snel, S. Francese, P. Scriven, V. Carolan and M. Clench, Novel molecular tumour classification using MALDI-mass spectrometry imaging of tissue micro-array, Anal Bioanal Biochem 397 (2010), 587-601.
22. J.M. Hillegass, A. Shukla, M.B. MacPherson, J.P. Bond, C. Steele and B.T. Mossman, Utilization of gene profiling and proteomics to determine mineral pathogenicity in a human mesothelial cell line (LP9/TERT-1), J Toxicol Environ Health A 73 (2010), 423-436.
23. E. Marengo, E. Robotti, M. Bobba and F. Gosetti, The principle of exhaustiveness versus the principle of parsimony: a new approach for the identification of biomarkers from proteomic spot volume datasets based on principal component analysis, Anal Bioanal Chem 397 (2010), 25-41.
24. M.P. Molloy, B.R. Herbert, B.J. Walsh, M.I. Tyler, M. Trai-ni, J.C. Sanchez, D.F. Hochstrasser, K.L. Williams and A.A. Gooley, Extraction of membrane proteins by differential sol-ubilization for separation using two-dimensional gel elec-trophoresis, Electrophoresis 19 (1998), 837-844. (Pubitemid 28236692)
25. M.I. Othman, M.I. Majid, M. Singh, S. Subathra, L. Seng and L.H. Gam, Proteomics of grade 3 infiltrating ductal carcinoma in Malaysian Chinese breast cancer patients, Biotechnol Appl Biochem 52 (2009), 209-219.
26. M. Laurière, A semidry electroblotting system effieciently transfers both high- and low-molecular weight proteins separated by SDS-PAGE, Anal Biochem 212 (1993), 206-211. (Pubitemid 23219475)
27. S. Sharma, Applied multivariate techniques, John Wiley and Sons, New York, 1996, pp. 241-244.
28. D.L. Massart, B.G.M. Vandeginste, L.M.C. Buydens, S. De Jong, P.J. Lewi and J. Smeyers-Verbeke, eds, Handbook of Chemometrics and Qualimetrics: Part A, Volume 20, Part 1, Elsevier Science, 1998.
29. M.R. Emmert-Buck, R.F. Bonner, P.D. Smith, R.F. Chuaqui, Z. Zhuang, S.R. Goldstein, R.A. Weiss and L.A. Liotta, Laser capture microdissection, Science 274 (1996), 998-1001. (Pubitemid 26398425)
30. A.S. Felix, J. Weissfeld, R. Edwards and F. Linkov, Future directions in the field of endometrial cancer research: the need to investigate the tumor microenvironment, Eur J Gynaecol Oncol 31 (2010), 139-144.
31. J.J.F. Hair, R.E. Anderson, R.L. Tatham and W.C. Black, Mul-tivariate data analysis, Prentice Hall, New Jersey, 1998, 245, 258, 260-262.
32. L. Bini, B. Magi, B. Marzocchi, F. Arcuri, S. Tripodi, M. Cin-torino, J.C. Sanchez, S. Frutiger, G. Hughes, V. Pallini, D.F. Hochstrasser and P. Tosi, Protein expression profiles in hu- man breast ductal carcinoma and histologically normal tissue, Electrophoresis 18 (1997), 2832-2841. (Pubitemid 28059956)
33. B. Franzén, S. Linder, A.A. Alaiya, E. Eriksson, K. Fujioka, A.C. Bergman, H. Jörnvall and G. Auer, Analysis of polypep-tide expression in benign and malignant human breast lesions, Electrophoresis 18 (1997), 582-587. (Pubitemid 27174451)
34. K. Chahed, M. Kabbage, B. Hamrita, C.L. Guillier, M. Trimeche, S. Remadi, L. Ehret-Sabatier and L. Chouchane, Detection of protein alterations in male breast cancer using two dimensional gel electrophoresis and mass spectrometry: The involvement of several pathways in tumorigenesis, Clin Chim Acta 388 (2008), 106-114. (Pubitemid 350266579)
35. H.A. Sarvaija, J.H. Yoon and I.M. Lazar, Proteome profile of the MCF7 cancer cell line: A mass spectrometric evaluation, Rapid Commun Mass Spectrom 20 (2006), 3039-3055. (Pubitemid 44569783)
36. S. Kageyama, T. Isono, H. Iwaki, Y. Wakabayashi, Y. Okada, K. Kontani, K. Yoshimura, A. Terai, Y. Arai and T. Yoshiki, Identification by proteomic analysis of calreticulin as a marker for bladder cancer and evaluation of the diagnostic accuracy of its detection in urine, Clin Chem 50 (2004), 857-866. (Pubitemid 38543664)
37. S.A. Fraser, M. Michalak, W.H. Welch and D. Hudig, Calreti-culin, a component of the endoplasmic reticulum and of cyto-toxic lymphocyte granules, regulates perforin-mediated lysis in the hemolytic model system, Biochem Cell Biol 76 (1998), 881-887. (Pubitemid 29318187)
38. S.A. Fraser, R. Karimi, M. Michalak and D. Hudig, Per-forin lytic activity is controlled by calreticulin, J Immunol 164 (2000), 4150-4155. (Pubitemid 30215072)
39. Z.D. Juranic, Z. Neskovic-Konstantinovic, T.P. Stanojkovic, Z. Zizak, T. Srdic, N. Stanojevic-Bakic, D. Milosevic and D. Jovanovic, The antitumorimmune responseinHER-2 positive, metastatic breast cancer patients, J Transl Med 3 (2005), 13.
40. D.A. Shaywitz, L. Orci, M. Ravazzola, A. Swaroop and C.A. Kaiser, Human SEC13Rp functions in yeast and is located on transport vesicles budding from the endoplasmic reticulum, J Cell Biol 128 (1995), 769-777.
41. B.L. Tang, F. Peter, J. Krijnse-Locker, G. Griffiths and W. Hong, The mammalian homology of yeast Sec13p is enriched in the intermediate compartment and is essential for protein transport from the endoplasmic reticulum to the Golgi apparatus, Mol Cell Biol 17 (1997), 256-266. (Pubitemid 26425615)
42. J.M. Cuezva, M. Krajewska, M.L. de Heredia, S. Krajews-ki, G. Santamaria, H. Kim, J.M. Zapata, H. Marusawa, M. Chamorro and J.C. Reed, The bioenergetic signature of cancer: A marker of tumor progression, Cancer Res 62 (2002), 6674-6681. (Pubitemid 35364137)
43. A. Isidoro, M. Martinez, P.L. Fernández, A.D. Ortega, G. San-tamaria, M. Chamorro, J.C. Reed and J.M. Cuezva, Alteration of the bioenergetic phenotype of mitochondria is a hallmark of breast, gastric lung and oesophageal cancer, Biochem J 378 (2004), 17-20. (Pubitemid 38299539)
44. O. Warburg, On the origin of cancer cells, Science 123 (1956), 309-314.
45. T.J. Schulz, R. Thierbach, A. Voigt, G. Drewes, B. Mietzn-er, P. Steinberg, A.F.H. Pfeiffer and M. Ristow, Induction of oxidative metabolism by mitochondrial frataxin inhibits cancer growth: Otto Warburg revisited, J Biol Chem 281 (2006), 977-981.
46. D.R. Green and J.C. Reed, Mitochondria and apoptosis, Science 281 (1998), 1309-1312. (Pubitemid 28406816)
47. S. Matsuyama, Q. Xu, J. Velours and J.C. Reed, The mito-chondrial F0F1-ATPase proton pump is required for function of the proapoptotic protein Bax in yeast and mammalian cells, Mol Cell 1 (1998), 327-336. (Pubitemid 128378881)
48. T.C. Huang, H.Y. Chang, C.H. Hsu, W.H. Kuo, K.J. Chang and H.F. Juan, Targeting therapy for breast carcinoma by ATP synthase inhibitor Aurovertin B, J Proteome Res 7 (2008), 1433-1444.
49. K. Chahed, M. Kabbage, L. Ehret-Sabatier, C. Lemaitre-Guillier, S. Remadi, J. Hoebeke and L. Chouchane, Expression of fibrinogen E-fragment and fibrin E-fragment is inhibited in the human infiltrating ductal carcinoma of the breast: The two-dimensional electrophoresis and MALDI-TOF mass spectrometry analyses, Int J Oncol 27 (2005), 1425-1431.
50. A. Gonçalves, B. Esterni, F. Bertucci, R. Sauvan, M. Cu-bizzoles, S. Granjeaud, C. Chabannon, G. Houvenaegel, J. Jacquemier, X.Y. Meng, E.T. Fung, D. Dirnbaum, D. Maran-inchi, P. Vines and J.P. Borg, Postoperative serum proteomic profiles and identification of biomarkers with prognosis value in high-risk early breast cancer patients, Breast Cancer Res 7 (2005), P05.03.
51. A.K. Fentz, M. Sporl, J. Spangenberg, H.J. List, C. Zornig, A. Dorner, P. Layer, H. Juhl and K.A. David, Detection of colorectal adenoma and cancerbasedontransthyretin and C3a-desArg serum levels, Proteomics Clin Appl1 (2007), 536-544.
52. M. Ehmann, K. Felix, D. Hartmann, M. Schnölzer, M. Nees, S. Vorderwülbecke, R. Bogumil, M. Büchler and H. Friess, Identification of potential markers for the detection of pancreatic cancer through comparative serum protein expression profiling, Pancreas 34 (2007), 205-214. (Pubitemid 46294796)
53. C. Gerner, W. Steinkellner, K. Holzmann, A. Gsur, R. Grimm, C. Ensinger, P. Obrist and G. Sauermann, Elevated plasma levels of crosslinked fibrinogen gamma-chain dimer indicate cancer-related fibrin deposition and fibrinolysis, Thromb Haemost 85 (2001), 494-501. (Pubitemid 32233025)
54. R.I. Somiari, S. Somiari, S. Russell and C.D. Shriver, Pro-teomics of breast carcinoma, J Chromatogr B 815 (2005), 215-225.
55. P.J. Simpson-Haidaris and B. Rybarczyk, The role of fibrino-gen as an extracellular matrix protein,Ann NY Acad Sci 936 (2001), 406-425. (Pubitemid 32613924)
56. C.G. Colpaert, P.B. Vermeulen, I. Benoy, A. Soubry, F. van Roy, P. van Beest, G. Goovaerts, l.Y. Dirix, P. van Dam, S.B. Fox, A.L. Harris and E.A. Marck, Inflammatory breast cancer shows angiogenesis with high endothelial proliferation rate and strong E-cadherin expression, Br J Cancer 88 (2003), 718-725. (Pubitemid 36411451)
57. A. Sahni, P.J. Simpson-Haidaris, S.K. Sahni, G.G. Vaday and C.W. Francis, Fibrinogen synthesized by cancer cells augments the proliferative effect of fibroblast growth factor-2 (FGF-2), J Thromb Haemost 6 (2008), 176-183.
58. J.S. Palumbo, K.W. Kombrinck, A.F. Drew, T.S. Grimes, J.H. Kiser, J.L. Degen and T.H. Bugge, Fibrinogen is an important determinant of the metastatic potential of circulating tumor cells, Blood 96 (2000), 3302-3309.